Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease

Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [B...

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Published iniScience Vol. 19; pp. 162 - 176
Main Authors Zhang, Li, Huang, Yuemeng, Wang, Meng, Guo, Yafen, Liang, Jing, Yang, Xiurong, Qi, Wenjing, Wu, Yanjun, Si, Jinglei, Zhu, Siran, Li, Zhe, Li, Ruiqiang, Shi, Chao, Wang, Shuo, Zhang, Qunjie, Tang, Zhonglin, Wang, Lixian, Li, Kui, Fei, Ji-Feng, Lan, Ganqiu
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 27.09.2019
Elsevier
Subjects
Biological Sciences
Gene Ontology
Genomic Analysis
Genomics
Omics
Sequence Analysis
Transcriptomics
Biological Sciences
Genomic Analysis
Transcriptomics
Genomics
Omics
Sequence Analysis
Gene Ontology
Online AccessGet full text
ISSN2589-0042
2589-0042
DOI10.1016/j.isci.2019.07.025

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Abstract Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. [Display omitted] •Bama miniature pig (BM) is one of the pig lines with the highest inbreeding coefficient•This atlas is a report on the chromosome-level genome assembly of miniature pig•Genomic analyses revealed genetic basis underlying BM's advantages to study diabetes•Some lncRNAs and mRNAs may be linked to resistance to diabetogenic environment Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics
AbstractList Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism.
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. : Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics Subject Areas: Biological Sciences, Gene Ontology, Genomic Analysis, Genomics, Omics, Sequence Analysis, Transcriptomics
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. [Display omitted] •Bama miniature pig (BM) is one of the pig lines with the highest inbreeding coefficient•This atlas is a report on the chromosome-level genome assembly of miniature pig•Genomic analyses revealed genetic basis underlying BM's advantages to study diabetes•Some lncRNAs and mRNAs may be linked to resistance to diabetogenic environment Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics
Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their distinct anatomy and physiology. For the last 30 years, we have been developing a laboratory Asian miniature pig inbred line (Bama miniature pig [BM]) from the primitive Bama xiang pig via long-term selective inbreeding. Here, we assembled a BM reference genome at full chromosome-scale resolution with a total length of 2.49 Gb. Comparative and evolutionary genomic analyses identified numerous variations between the BM and commercial pig (Duroc), particularly those in the genetic loci associated with the features advantageous to diabetes studies. Resequencing analyses revealed many differentiated gene loci associated with inbreeding and other selective forces. These together with transcriptome analyses of diabetic pig models provide a comprehensive genetic basis for resistance to diabetogenic environment, especially related to energy metabolism. • Bama miniature pig (BM) is one of the pig lines with the highest inbreeding coefficient • This atlas is a report on the chromosome-level genome assembly of miniature pig • Genomic analyses revealed genetic basis underlying BM's advantages to study diabetes • Some lncRNAs and mRNAs may be linked to resistance to diabetogenic environment Biological Sciences; Gene Ontology; Genomic Analysis; Genomics; Omics; Sequence Analysis; Transcriptomics
Author Wang, Shuo
Fei, Ji-Feng
Li, Zhe
Zhang, Li
Si, Jinglei
Li, Ruiqiang
Wang, Meng
Yang, Xiurong
Shi, Chao
Li, Kui
Wu, Yanjun
Zhang, Qunjie
Qi, Wenjing
Zhu, Siran
Liang, Jing
Lan, Ganqiu
Huang, Yuemeng
Guo, Yafen
Wang, Lixian
Tang, Zhonglin
AuthorAffiliation 8 Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
9 Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
2 College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
6 Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
1 College of Animal Science and Technology, Guangxi University, Nanning 530004, China
7 Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
3 Novogene Bioinformatics Institute, Beijing 100083, China
4 Shandong Provincial Key Laboratory of Biochemical Engineering, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
5 Institution of Genomics and Bioinformatics, South China Agricultural Univers
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  organization: College of Animal Science and Technology, Guangxi University, Nanning 530004, China
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31376679$$D View this record in MEDLINE/PubMed
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Keywords Biological Sciences
Genomic Analysis
Transcriptomics
Genomics
Omics
Sequence Analysis
Gene Ontology
Language English
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Snippet Pig has been proved to be a valuable large animal model used for research on diabetic disease. However, their translational value is limited given their...
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SubjectTerms Biological Sciences
Gene Ontology
Genomic Analysis
Genomics
Omics
Sequence Analysis
Transcriptomics
Title Development and Genome Sequencing of a Laboratory-Inbred Miniature Pig Facilitates Study of Human Diabetic Disease
URI https://dx.doi.org/10.1016/j.isci.2019.07.025
https://www.ncbi.nlm.nih.gov/pubmed/31376679
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